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ExpressionBlast: mining large, unstructured expression databases

Nature Methods volume 10, pages 925–926 (2013)Cite this article

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To the Editor:

The amount of gene expression data deposited in public repositories has grown exponentially over the last decade (Supplementary Fig. 1). Specifically, Gene Expression Omnibus (GEO)1 is one of largest expression-data repositories (Supplementary Table 1), containing hundreds of thousands of microarray and RNA-seq experiment results grouped into tens of thousands of series. Although accessible, data deposited in GEO are not well organized. Even among data sets for a single species there are many different platforms with different probe identifiers, different value scales and very limited annotations of the condition profiled by each array. Current methods for using GEO data to study signaling and other cellular networks either do not scale or cannot fully use the available information (Supplementary Table 2 and Supplementary Results).

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Figure 1: Data processing and tool usage.

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Acknowledgements

This work was supported in part by US National Institutes of Health grant 1RO1 GM085022 and US National Science Foundation awards DBI-0965316 and I-Corps 1242525 to Z.B.-J.

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Author notes

  1. Guy E Zinman and Shoshana Naiman: These authors contributed equally to this work.

Authors and Affiliations

  1. Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

    Guy E Zinman & Ziv Bar-Joseph

  2. The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel

    Shoshana Naiman, Yariv Kanfi & Haim Cohen

Authors
  1. Guy E Zinman
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  2. Shoshana Naiman
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  3. Yariv Kanfi
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  5. Ziv Bar-Joseph
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Corresponding author

Correspondence to Ziv Bar-Joseph.

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Supplementary Figures 1 and 2, Supplementary Tables 1–4, Supplementary Results and Supplementary Methods (PDF 792 kb)

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Zinman, G., Naiman, S., Kanfi, Y. et al. ExpressionBlast: mining large, unstructured expression databases. Nat Methods 10, 925–926 (2013). https://doi.org/10.1038/nmeth.2630

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